PHOENIX — The Border Patrol agent assaulted her after she crossed into Texas' Rio Grande Valley from Mexico, the woman said, and she insisted on filing a complaint. She did so on May 20, 2009.

Nearly three years later, the investigation of that complaint by Customs and Border Protection's Office of Internal Affairs was "still pending," according to CBP documents.

Her case was anything but unique.

Out of 809 complaints of abuse filed against Border Patrol agents from January 2009 to January 2012, only 13 resulted in any kind of action by the CBP. Two complaints led to court action and one more to an agent's suspension. Six resulted in "counseling," according to documents obtained through Freedom of Information Act requests by the American Immigration Council, a Washington, D.C.-based immigrant-advocacy group.

Forty percent of the complaints were still pending investigation when the CBP turned over the documents.

Researchers said they couldn't determine which complaints had merit, but their analysis showed that CBP officials rarely take actions against agents alleged to have engaged in abusive behavior. The complaints to Internal Affairs are an unknown fraction of overall complaints, researchers said, because the CBP doesn't tie together the various ways people can file complaints into a single, unified system, and it doesn't track all complaints.

"Border Patrol agents who commit abuse simply get away with it," said Vicki Gaubeca of the American Civil Liberties Union's Regional Center for Border Rights in New Mexico.

She said the abuse report ties in with earlier studies and research showing that "there's a pattern of civil- and human-rights abuses, ranging from racial profiling, excessive force, invasive searches, unjustified detentions, and use of coercion to force people to surrender their rights."

"These abuses are against undocumented immigrants, legal residents and American citizens," she said.

An ongoing investigation by The Arizona Republic has found at least 44 cases since 2005 in which Border Patrol agents or customs officers killed people, but no instances in which an agent or officer was known to have been disciplined for the deaths.

CBP officials didn't respond by deadline to repeated requests by The Republic for comment on the abuse complaints. In previous discussions of abuse allegations, CBP officials dismissed the idea of a systemic problem. Over the period covered by the abuse complaints, Border Patrol agents made more than 900,000 apprehensions.

The numbers would seem to indicate a ratio of roughly one complaint per 1,000 apprehensions. But "this data is just scratching the surface of the problem," said Daniel Martinez, a sociologist at George Washington University who co-authored the report for the council on the abuse-complaint data.

He said many migrants don't know where or how to file abuse complaints. They may fear retaliation.

Jennifer Podkul, a program officer with the Women's Refugee Commission, said she recently visited a Border Patrol facility that had a poster explaining how to file a complaint. It gave a non-working phone number for the Immigration and Naturalization Service, an agency dissolved 11 years ago.

Three studies by different organizations in recent years, based on interviews with hundreds of migrants deported back to Mexico, found similar rates of reported problems, with about 10 percent of migrants reporting being physically abused by agents. That would imply about 90,000 abuse incidents over the time period covered by the reports.

Whatever the numbers, the summaries of some of the incidents included in the data Martinez and the other researchers collected are striking.

More than 60 complaints reported that agents kicked or stomped on detainees — including one case in which an agent allegedly kicked a pregnant woman and caused her to miscarry. Fourteen detainees reported groping or improper touching; six women reported being sexually abused, and other women said they were forced to strip or show agents their breasts.

Fifty-eight cases involved alleged abuse of minors. One youth said an agent "hit him on the head with a metal flashlight 20 times; kicked him 5 times; and pushed him down a hill."

More than one-third of the complaints were filed in the Tucson Sector, but that sector also had by far the highest volume of apprehensions from 2009 to 2012. The Del Rio and Rio Grande Valley sectors in Texas had the highest rate of complaints as a percentage of apprehensions, followed by the San Diego Sector.

The immigration council, ACLU and 14 other civil- and immigrant-rights groups have submitted recommendations to the Department of Homeland Security. They called on officials to create a single, unified complaint system that allows filing complaints online, through mobile phones and telephones through a toll-free number; to develop a unified process for receiving and investigating complaints; to make information about complaints more available to the public — and to analyze data about complaints to improve policies and training.

Podkul said CBP officials agreed to meet with advocates next month.

Researcher Martinez said that the policy discussions in Washington are out of touch with the realities people are experiencing along the border. He said that in 2008, while he was doing field work for an earlier study on how migrants are treated, he and his colleagues were stopped by CBP officers as they were crossing into Mexico at the main port of entry in Nogales.

"I asked the guy, 'Why are you stopping me?' He accused us of being smugglers and said that, for all intents and purposes, we had no rights and he could make our life hell. ... If people understood the police state in which people along the border live, they'd be furious."